I think I am using the cleanup tool wrong cause either it does nothing or it collapses the whole model. So in the end smoothing and looking for strange bumps was the best way for me to find extra vertices.

This is perhaps more of a philosophical question, but do models have to be perfect or will they render just as good if one piles up a number of different "boxes" that intersect? I mean you could make a T-shape with extrudes that are connected or simply stacking two qubes? Does it matter in the end? Assuming you will not animate the object?

That being said the topology should be clean (no floating verts, non-manifold geometry, co-planar faces, faces with zero surface area, etc. These are the things that cause Maya's tools to malfunction and others done the pipeline to want to put a hit contract out on you!

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"If I have seen further it is by standing on the shoulders of giants." Sir Isaac Newton, 1675

Not really. It depends on your clients or your own needs. As someone else said if there are no written requirements then it all really comes down to doing it however you can to get results you or your client are happy with.

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"If I have seen further it is by standing on the shoulders of giants." Sir Isaac Newton, 1675

The quickest way usually is to just use the split poly tool, and extrude the polys afterwards. Doing this will also always give you better geometry than booleans, which will always create n-sided polys.

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